Publications

denotes joint authorship. $ denotes corresponding author.

Sorted by year

Submitted and In Preparation

  • GAMer 2: A System for 3D Mesh Processing of Cellular Electron Micrographs

    C. T. Lee†,$, J. G. Laughlin, N. Angliviel de La Beaumelle, R. E. Amaro, J. A. McCammon, R. Ramamoorthi, M. J. Holst, and P. Rangamani$
    In Review
    arXiv bioRxiv More info →

Peer Reviewed and In Press

  1. An Open Source Mesh Generation Platform for Biophysical Modeling Using Realistic Cellular Geometries

    C. T. Lee$, J. G. Laughlin, J. B. Moody, R. E. Amaro, J. A. McCammon, M. J. Holst, and P. Rangamani$
    Biophysical Journal, 2020
    DOI arXiv bioRxiv More info →

  2. Applications and Challenges of Machine Learning to Enable Realistic Cellular Simulations

    R. Vasan, M. P. Rowan, C. T. Lee, G. R. Johnson, P. Rangamani, and M. J. Holst$
    Frontiers in Physics, 2020
    DOI arXiv More info →

  3. The Implementation of The Colored Abstract Simplicial Complex and its Application to Mesh Generation

    C. T. Lee†,$, J. B. Moody, R. E. Amaro, J. A. McCammon, and M. J. Holst
    ACM Transactions on Mathematical Software, 2019
    DOI arXiv More info →

  4. Exascale Computing will be a New Dawn for Computational Biology

    C. T. Lee, and R. E. Amaro$
    Computing in Science and Engineering, 2018
    DOI More info →

  5. Quantitative Ranking of β-cyclodextrin Ligand Binding Kinetics With SEEKR, a Hybrid MD/BD/Milestoning Approach

    B.R. Jagger, C. T. Lee, R. E. Amaro$
    The Journal of Physical Chemistry Letters, 2018
    DOI ChemRxiv: ChemRxiv More info →

  6. Structural Basis for Ligand Modulation of CCR2 Activation Pathways

    B.C. Taylor, C. T. Lee, and R. E. Amaro$
    Proceedings of the National Academy of Sciences, 2018
    DOI bioRxiv More info →

  7. Two Relations to Estimate Membrane Permeability Using Milestoning

    L. W. Votapka, C. T. Lee, and R. E. Amaro$
    Journal of Physical Chemistry B, 2016
    DOI More info →

  8. Emerging Computational Methods for the Rational Discovery of Allosteric Drugs

    J. R. Wagner, C. T. Lee, J. D. Durrant, R. D. Malmstrom, V. A. Feher, and R. E. Amaro$
    Chemical Reviews, 2016
    DOI More info →

  9. Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds

    C. T. Lee, J. Comer, C. Herndon, N. Leung, A. Pavlova, R. V. Swift, C. Tung, C. N. Rowley, R. E. Amaro$, C. Chipot$, Y. Wang$, and J. C. Gumbart$
    Journal of Chemical Informatics and Modeling, 2016
    DOI More info →

  10. Known structure, unknown function: An inquiry-based undergraduate biochemistry laboratory course

    C. Gray, C. W. Price, C. T. Lee, A. H. Dewald, M. A. Cline, C. E. McAnany, L. Columbus$, and C. Mura$
    Biochemistry and Molecular Biology Education, 2015
    DOI More info →

  11. Application of Molecular-Dynamics Based Markov State Models to Functional Proteins

    R. D. Malmstrom, C. T. Lee, A. T. Van Wart, and R. E. Amaro$
    Journal of Chemical Theory and Computation, 2014
    DOI More info →